We are interested in the study of enzyme function, primarily at the levels of catalytic and specificity mechanisms, with a long term goal of developing enzyme inhibitors with potential therapeutic application. The current focus is on both bacterial and mammalian enzymes involved in the epigenetic process of DNA methylation. A second focus of the lab combines bio-inspired molecular assembly concepts with novel inorganic materials to develop nano-electronics, new biophysical and cell-biology tools, and novel sensors.

DNA methyltransferases: epigenetics, enzyme mechanisms, and the development of novel therapeutics

S-Adenosyl methionine-dependent DNA methyltransferases modify DNA sequence-specifically. Bacterial DNA is modified at both cytosine (N4 or C5) and adenine (N6), while mammalian DNA is modified only at cytosine C5. The bacterial enzymes are involved in restriction/modification, mismatch repair, replication timing, and gene regulation. These enzymes are essential to the virulence of several human pathogens. Numerous high resolution x-ray structures are available for these bacterial enzymes, enabling our efforts to understand the following aspects:
  1. Mechanisms of catalysis
  2. Importance of conformational mechanisms, including DNA bending, base flipping, intercalation, and protein loop motion towards catalysis and specificity.
  3. The importance of correlated protein motion to catalysis, and the use of such information to identify allosteric sites which may form the basis of designing allosteric inhibitors.
  4. Antibiotic design based on inhibiting the bacterial DNA MTases.
  5. Determining how DNA methylation regulates virulence in the major causative microbe which causes periodontitis, Actinobacillus actinomycetomcomitans.

Mammalian DNA methylation is involved in parent of origin imprinting, x-chromosome inactivation, host defense, and tissue-specific gene regulation. Aberrant DNA methylation of tumor suppressor genes is a primary and early event in human tumorigenesis. A major unresolved question is how do the patterns of DNA methylation, which occur in the CpG dinucleotide, become established? Recent work shows that the mammalian DNA cytosine methyltransferases (Dnmt1, Dnmt2, Dnmt3 family) interact with other cellular proteins, and that de novo DNA methylation is directed in part by non-coding RNA. Our efforts are focused on studying the human enzymes to understand how interactions with other proteins and RNA direct the function and specificity of these enzymes. We have also identified inhibitors of the mammalian enzymes which are cell active.

A related effort to both the bacterial and mammalian enzyme studies is the development of new bio-assays. We recently developed a new energy transfer technology involving metallic nanoparticles (e.g., gold) and fluorescent dyes to detect the assembly of multiple proteins on DNA over distances not presently attainable by classic FRET methods. The use of this technology to detect gene regulatory assemblies in cells is ongoing.

Bio-inspired assembly of inorganic materials: Bio-Sensors and Nano-Electronics

Modern molecular biology techniques allow the creation of templates and materials of very exacting reactivity, size, structure, and periodicity. These materials can be usefully coupled to inorganic compounds to create bio-materials that are active and well-controlled on a molecular scale. Currently, our investigations are most concerned with utilizing the programmability and specificity of DNA, coupled with the ability to stoichiometrically decorate homogeneous metallic nanoparticles, towards the creation of novel bio-sensor and nano-electronics components with tightly controlled electrical and optical properties.